“整合物种概念”和“分化路上的物种”

已有的各个物种概念对物种的认识类似盲人摸象, 只包含了物种的某一个方面; 而一个分化后期的成熟物种应涵盖了所有的物种概念。但是, 尚未到达分化后期的物种往往又已开始新一轮的物种分化; 自然中存在的多数“物种”处于分化路上。这种循环往复连续分化产生的物种, 存在种间生殖隔离不彻底、基因流频繁发生、网状进化突出等现象。此外, 对于不同的物种对, 最早开始分化的基因以及不同物种概念所要求的条件的分化顺序不是统一的, 而是随机的。定义一个适合所有“分化路上的物种”概念存在较大困难。但是, 应采用尽可能多的物种概念来界定分化路上的物种、发表新种和进行分类处理; 也应承认种间可能广泛存在不完全的生殖隔离和有限的基因流, 即有不属于两个物种群体的杂交或回交个体的存在。这样划分的物种比只依据一个物种概念认定的物种具有更高的客观性和科学性。     

“地衣”词考

本文考证了中国先秦时期到清末古籍中对“地衣”的解释;其中有共生学意义的“地衣”一词,是在清代李善兰的《植物学》一书中被提出的。     

“Ryanopathies” and RyR2 dysfunctions: can we further decipher them using in vitro human disease models?

The regulation of intracellular calcium (Ca²⁺) homeostasis is fundamental to maintain normal functions in many cell types. The ryanodine receptor (RyR), the largest intracellular calcium release channel located on the sarco/endoplasmic reticulum (SR/ER), plays a key role in the intracellular Ca²⁺ handling. Abnormal type 2 ryanodine receptor (RyR2) function, associated to mutations (ryanopathies) or pathological remodeling, has been reported, not only in cardiac diseases, but also in neuronal and pancreatic disorders. While animal models and in vitro studies provided valuable contributions to our knowledge on RyR2 dysfunctions, the human cell models derived from patients’ cells offer new hope for improving our understanding of human clinical diseases and enrich the development of great medical advances. We here discuss the current knowledge on RyR2 dysfunctions associated with mutations and post-translational remodeling. We then reviewed the novel human cellular technologies allowing the correlation of patient’s genome with their cellular environment and providing approaches for personalized RyR-targeted therapeutics.Subject terms: Ventricular tachycardia, Ventricular tachycardia     

“瑞草”灵芝之现代研究

"灵芝"一词最早出现于东汉,人们"以为瑞草,服之神仙",称之为"灵芝"。现指隶属于真菌界Fungi、担子菌门Basidiomycota、伞菌纲Agaricomycetes、多孔菌目Polyporales、灵芝科Ganodermataceae的一类传统药用真菌的统称,具有免疫调节、抗肿瘤、抗氧化、抑菌、保肝护肝、止咳平喘等多种功效(林志彬2015;Gilletal.2016;Ahmad2018;Wuetal.     

“超级真菌”耳念珠菌研究进展

耳念珠菌Candida auris也被称为“超级真菌”,是近年来出现的一种人体病原真菌新物种,临床分离株通常具有多重耐药和高致死率等特征。2009年日本首次报道耳念珠菌之后,其感染病例在多个国家呈现出爆发式增长。目前已报道的病例分布在全球五大洲27个国家,包括中国。耳念珠菌感染给临床诊断和防控以及人类健康带来了巨大的挑战。本文从该菌临床分离菌株的生物学、遗传变异分化及耐药特征等方面入手,围绕分子流行病学、基因组特征、毒性因子和耐药性等方面系统地综述了近年来国内外取得的相关进展,并探讨了我国耳念珠菌感染的诊断、治疗和预防的措施。     

N2(C2H2−C2H4) fixation in two species of Ceanothus seedlings in second year postfire chaparral

Nitrogen fixation in excised root nodules of 2-year-old, postfireCeanothus tomentosus andC. leucodermis seedlings was measured over an 8-month period using the acetylene reduction method. High levels of NO₃–N and NH₄–N present in postfire soils were limited to the upper 10 cm and did not inhibit nodulation in these deeper-rooting seedlings. Decreases in acetylene reduction activity occurred with decreased soil moisture and increased soil temperature. Nitrogen gains from these two Ceanothus shrub seedlings totalled 1.6 kg N ha^–1 yr^–1.     

Elacestrant in metastatic breast cancer: Is the “standard of care” meeting standard requirements?

The EMERALD trial was an open label phase 3 trial evaluating elacestrant, the first oral selective estrogen receptor degrader (SERD), as compared to “standard of care”, in ER+/HER2- (hormone receptor positive, no HER2 overexpression) advanced or metastatic breast cancer.The EMERALD trial restricted the “standard of care” control arm to limited options that may have led to a substandard control arm. We describe how the EMERALD trial protocol allowed different clinically inappropriate scenarios in the control arm, according to prior therapy. The main relevant question remains the potential advantage of elacestrant over fulvestrant in fulvestrant-naive patients.Analyzing outcomes in subgroups according to prior and per-protocol therapy would help analyzing trial results. However, these subgroup results may be non-significant, and another randomized trial will be needed. Trials should be designed to answer directly clinical questions that are relevant.     

新医学是解决人类健康问题的真正钥匙——需“精准”理解奥巴马的“精准医学计划”

2015年年初,美国总统奥巴马在国情咨文中提出了一个预算2.15亿美元的“精准医学计划”,希望以此“引领一个医学时代”。新闻一经发布,“精准医学”立刻成为了媒体和百姓嘴边的热词,受此影响国内亦有不少人士纷纷为美国总统的这一计划点“赞”。有人用“医学革命”来形容它,有人用“开创性”来抬高它,还有一个传闻,受奥巴马“精准医学计划”的影响,中国将在15年内投入600亿元人民币启动并发展中国版的“精准医学计划”。对此,有人提出了质疑,美国版精准医学计划是否符合中国国情?是否存在“水土不服”的可能?直接套用美国总统的智慧能否解决具有中国特色的实际问题?争论由此引发一个让人思考的问题,究竟什么才是现代医学的核心?在盲目堆钱的行动前,我们确实有必要从科学和临床应用的角度来探讨和思考一下现代医学的发展方向。 为了能“精准”地看到问题的实质,我将从当下时髦并且相关的词汇谈起,通过梳理,期待找出解决人类健康问题的真正钥匙。     

Microclimate‐driven trends in spring‐emergence phenology in a temperate reptile (Vipera berus): Evidence for a potential “climate trap”?

Climate change can not only increase the exposure of organisms to higher temperatures but can also drive phenological shifts that alter their susceptibility to conditions at the onset of breeding cycles. Organisms rely on climatic cues to time annual life cycle events, but the extent to which climate change has altered cue reliability remains unclear. Here, we examined the risk of a “climate trap”—a climatically driven desynchronization of the cues that determine life cycle events and fitness later in the season in a temperate reptile, the European adder (Vipera berus). During the winter, adders hibernate underground, buffered against subzero temperatures, and re‐emerge in the spring to reproduce. We derived annual spring‐emergence trends between 1983 and 2017 from historical observations in Cornwall, UK, and related these trends to the microclimatic conditions that adders experienced. Using a mechanistic microclimate model, we computed below‐ and near‐ground temperatures to derive accumulated degree‐hour and absolute temperature thresholds that predicted annual spring‐emergence timing. Trends in annual‐emergence timing and subsequent exposure to ground frost were then quantified. We found that adders have advanced their phenology toward earlier emergence. Earlier emergence was associated with increased exposure to ground frost and, contradicting the expected effects of macroclimate warming, increased post‐emergence exposure to ground frost at some locations. The susceptibility of adders to this “climate trap” was related to the rate at which frost risk diminishes relative to advancement in phenology, which depends on the seasonality of climate. We emphasize the need to consider exposure to changing microclimatic conditions when forecasting biological impacts of climate change.     

Molecular Evolution of Human H1N1 and H3N2 Influenza A Virus in Thailand, 2006–2009

Background

Annual seasonal influenza outbreaks are associated with high morbidity and mortality.

Objective

To index and document evolutionary changes among influenza A H1N1 and H3N2 viruses isolated from Thailand during 2006–2009, using complete genome sequences.

Methods

Nasopharyngeal aspirates were collected from patients diagnosed with respiratory illness in Thailand during 2006–2009. All samples were screened for Influenza A virus. A total of 13 H1N1 and 21 H3N2 were confirmed and whole genome sequenced for the evolutionary analysis using standard phylogenetic approaches.

Results

Phylogenetic analysis of HA revealed a clear diversification of seasonal from vaccine strain lineages. H3N2 seasonal clusters were closely related to the WHO recommended vaccine strains in each season. Most H1N1 isolates could be differentiated into 3 lineages. The A/Brisbane/59/2007 lineage, a vaccine strain for H1N1 since 2008, is closely related with the H1N1 subtypes circulating in 2009. HA sequences were conserved at the receptor-binding site. Amino acid variations in the antigenic site resulted in a possible N-linked glycosylation motif. Recent H3N2 isolates had higher genetic variations compared to H1N1 isolates. Most substitutions in the NP protein were clustered in the T-cell recognition domains.

Conclusion

In this study we performed evolutionary genetic analysis of influenza A viruses in Thailand between 2006–2009. Although the current vaccine strain is efficient for controlling the circulating outbreak subtypes, surveillance is necessary to provide unambiguous information on emergent viruses. In summary, the findings of this study contribute the understanding of evolution in influenza A viruses in humans and is useful for routine surveillance and vaccine strain selection.     

1H-1H correlations across N–H•••N hydrogen bonds in nucleic acids

In 2HJ(NN)-COSY experiments, which correlate protons with donor/acceptor nitrogens across Nd...HNa bonds, the receptor nitrogen needs to be assigned in order to unambiguously identify the hydrogen bond. For many situations this is a non-trivial task which is further complicated by poor dispersion of (Na,Nd) resonances. To address these problems, we present pulse sequences to obtain direct, internucleotide correlations between protons in uniformly 13C/15N labeled nucleic acids containing Nd...HNa hydrogen bonds. Specifically, the pulse sequence H2(N1N3)H3 correlates H2(A,omega1):H3(U,omega2) protons across Watson-CrickA-U and mismatched G.A base pairs, the sequences H5(N3N1)H1/H6(N3N1)H1 correlate H5(C,omega1)/H6(C,omega1):H1(G,omega2) protons across Watson-Crick G-C base pairs, and the H2(N2N7)H8 sequence correlates NH2(G,A,C;omega1):H8(G,A;omega2) protons across G.G, A.A, sheared G.A and other mismatch pairs. These 1H-1H connectivities circumvent the need for independent assignment of the donor/acceptor nitrogen and related degeneracy issues associated with poorly dispersed nitrogen resonances. The methodology is demonstrated on uniformly 13C/15N labeled samples of (a) an RNA regulatory element involving the HIV-1 TAR RNA fragment, (b) a multi-stranded DNA architecture involving a G.(C-A) triad-containing G-quadruplex and (c) a peptide-RNA complex involving an evolved peptide bound to the HIV-1 Rev response element (RRE) RNA fragment.     

荒漠草原“土岛”生境群落物种共存机制

经过长期破碎化, 荒漠草原原生硬质灰钙土斑块散布在广大沙化土地中, 形成类似“土岛”的土被结构。为揭示土岛生境的群落物种共存机制, 2016年在宁夏盐池县皖记沟村选取大(200-300 m²)、中(约100 m²)、小(约50 m²)土岛各3个开展调查, 采用Jaccard相异系数、物种生态位宽度和生态位重叠度、零模型、Meta分析, 综合计算和分析土岛内部与外部植物群落相似性、物种生态位宽度和生态位重叠、物种共存格局及其影响因子。研究发现, (1)随着破碎化加剧, 土岛内部植物多样性整体呈现下降趋势, 群落优势种从短花针茅(Stipa breviflora)转变为猪毛蒿(Artemisia scoparia)和短花针茅共优种, 土岛内外群落相似性增加。(2)土岛内外绝大多数物种生态位重叠较小, 生态位重叠在土岛内呈集中分布, 而土岛外则呈均匀发散分布。(3)环境过滤为主的生态过程决定了土岛生境群落物种的共存格局, 随着土岛面积减小, 环境因子对群落物种共存的调控强度降低, 关键性环境因子由土壤细砂粒和黏粒转变为粗砂粒, 显著性竞争物种共存格局在小岛出现。综上所述, 土岛生境对于维持草原物种具有重要作用, 环境过滤主导了荒漠草原物种共存格局。随着生境破碎化加剧或土岛面积减小, 物种共存格局及其调控因子发生转变。保护面积在200 m²以上的大土岛对于恢复荒漠草原区草原成分种和其物种多样性机制都十分必要。